MolNFT v1 · #46240 · protein

Crystal structure of putative dioxygenase (YP_555069.1) from burkholderia xenovorans LB400 at 1.70 a resolution

2NYH: “Crystal structure of putative dioxygenase (YP_555069.1) from burkholderia xenovorans LB400 at 1.70 a…”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.40). MolNFT v1 #46240 on GenesisL1: 3D structure, binding…

PDB: 2NYH
Type: protein
Length: 231 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative dioxygenase
UniProt: Q13JM0
Ligands: SO4
Pockets: 2 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative dioxygenase	protein	116	37% helix, 23% strand	Q13JM0
B	Putative dioxygenase	protein	115	38% helix, 23% strand	Q13JM0

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.40	0.78	23	empty
2	56	0.33	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 1400 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

2NYH · Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia Xenovorans… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q13JM0
Elsewhere: RCSB PDB 2NYH · PDBe 2NYH · UniProt Q13JM0

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